Search for: All records

ABSTRACT Adaptive introgression involves the acquisition of advantageous genetic variants through hybridisation, which are subsequently favoured by natural selection due to their association with beneficial traits. Here, we analysed speciation patterns of the kleptoparasitic spider,Argyrodes lanyuensis, through genomic analyses and tested for possible genetic evidence of adaptive introgression at the Taiwan–Philippines transition zone. Our study used highly polymorphic SNPs to demonstrate that speciation occurred when the Hualien (on Taiwan Island + Green Island) and Orchid Island + Philippine lineages separated during the early to mid‐Pleistocene. The best colonisation model suggested by approximate Bayesian computation and random forests and biogeographical analyses supported an inference of a bottleneck during speciation, an interpretation reinforced by observation of lowerF_STvalues and reduced genetic diversity of the Orchid Island + Philippines lineage. We also found the highest support for the occurrence of introgression on the youngest island (Green Island) of the Taiwan–Philippines transition zone based on the ABBA‐BABA test. Our study highlights the inference of two noteworthy species (Hualien + Green Island and Orchid Island + Philippines) based on our species delimitation tests, with gene flow between Green Island and Orchid Island that indicates introgression. The potential adaptive alleles in Green Island population, which are under balancing selection, provide initial evidence of possible rare case of adaptive introgression. This could represent an evolutionary response to a newly formed niche (or novel geographical context) lying between the tropical climate of the Philippines and the subtropical climate of Hualien, Taiwan. 

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former ‘Out of Africa’ hypothesis and support an ‘Out of Asia’ scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe. 

Characterization of species distributions is a fundamental challenge in biodiversity science, with particular significance for downstream evolutionary studies, conservation efforts, field-based faunal studies and estimates of species diversity. Checklists and phylogenetic studies often focus on poorly known, rare taxa with limited ranges. However, studies of widely distributed, ecologically important species that are abundant in their preferred microhabitats are also important for systematics and local conservation efforts, but less often studied. We collected novel natural history data during fieldwork (2019–2023) for Philippine populations of bockadams (Homalopsidae:Cerberus), one of the most abundant vertebrates in Southeast Asian aquatic systems. Considered a coastal snake, many studies reportCerberusinland. We report the frequency of encounters ofCerberus schneiderii, and the IUCN data-deficient, Philippine-endemicCerberus microlepisduring six expeditions (62 days; 1041 person-hours). We report new occurrence data for 69C. schneideriiand6 C. microlepisfor coastal and inland populations, water measurements and dietary observations. Regression analyses and ecological niche models show the importance of coastal and mangrove habitats forCerberus. Our study is the most comprehensive assessment of PhilippineCerberuspopulations to date and provides critical baseline natural history data for downstream research on widespread and range-restricted species of Southeast Asian snakes. 

Abstract Although the differentiation of clades at the species level is usually based on a justifiable and testable conceptual framework, the demarcation of supraspecific boundaries is less objective and often subject to differences of opinion. The increased availability of large-scale phylogenies has in part promulgated a practice of what we consider excessively splitting clades at the “genus” level. Many of these new genus-level splits are predicated on untenable supporting evidence (e.g., weakly supported phylogenies and purportedly “diagnostic” but actually variable, non-exclusive, or otherwise problematic opposing character state differences) without careful consideration of the effects on downstream applications. As case studies, we critically evaluate several recent examples of splitting established monophyletic genera in four amphibian families that resulted in the creation/elevation of 20 genus-level names (Dicroglossidae:Phrynoglossus,Oreobatrachus,Frethiasplit fromOccidozyga; Microhylidae:Nanohylasplit fromMicrohyla; Ranidae:Abavorana,Amnirana,Chalcorana,Humerana,Hydrophylax,Indosylvirana,Papurana,Pulchrana,Sylviranasplit fromHylarana; Rhacophoridae:Tamixalus,Vampyrius,Leptomantis,Zhangixalussplit fromRhacophorus,Rohanixalussplit fromFeihyla,Orixalussplit fromGracixalus, andTarugasplit fromPolypedates), and also address the taxonomic status of the monotypic genusPteroranarelative toHylarana. We reassess the original claims of diagnosability and justifications for splitting and argue that in many cases, the generic splitting of clades is not only unnecessary but also destabilizes amphibian taxonomy, leading to a host of downstream issues that affect categories of the user community (stakeholders such as taxonomists, conservationists, evolutionary biologists, biogeographers, museum curators, educators, and the lay public). As an alternative, we advocate for the use of the subgenus rank in some cases, which can be implemented to establish informative partitions for future research without compromising on information content, while avoiding gratuitous (and often transient) large-scale binomial (genus-species couplet) rearrangements. We encourage taxonomists to consider the actual needs and interests of the larger non-taxonomic end-user community who fund the majority of taxonomic research, and who require a system that remains reasonably stable and is relatively intuitive, without the need for inaccessible laboratory equipment or advanced technical scientific knowledge to identify amphibian species to the genus level. 

A first review of the history, status, and prospects for Philippine herpetology conducted more than two decades ago (2002) summarized the diverse topics studied and highlighted the development and achievements in research up to the year 2000. This study revisits and re-assesses what Philippine herpetology has accomplished, both as a discipline and a community, during the last two decades (2002–2022). A total of 423 herpetological publications was collated, revealing a substantial increase in annual publications, rising from approximately four per year during 2002–2008 to around 28 per year in 2009–2022. Half of the published studies focused on squamate reptiles (lizards 30.5%, snakes 21%) and 28.4% on amphibians, 5.9% on turtles, and 2.6% on crocodiles. The remaining 11.6% of studies focused simultaneously on multiple taxa (i.e., faunal inventories). Diversity and distribution (35.2%) and ecological (26.5%) studies remained popular, while studies on taxonomy (14.9%), phylogenetics and biogeography (11.8%), and conservation (11.6%) all increased. However, geographical gaps persist urging immediate surveys in many understudied regions of the country. Finally, we found a balanced representation between Filipino and foreign first authors (1.0:1.1), yet a substantial gender gap exists between male and female first authors (7.1:1.0). Nonetheless, the steep increase in publications and the diversity of people engaged in Philippine herpetology is a remarkable positive finding compared to the 20 years preceding the last review (1980–2000). Our hope is that the next decades will bring increasingly equitable, internationally collaborative, and broadly inclusive engagement in the study of amphibians and reptiles in the Philippines. 

The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.